Paolo Guerrero’s 69th-minute header won it for the Brazilian side in Yokohama after Gary Cahill, Eden Hazard, Fernando Torres and Juan Mata all spurned good openings for the Champions League holders.
Torres saw his header ruled out for offside in the dying moments, before Cahill was shown a straight red card late on for an apparent elbow on Emerson.
Benítez, whose side have had chances to win the Community Shield and the Uefa Super Cup ahead of this tournament in Japan, felt the Blues performed well and created enough chances to win the game.
“Against a good team we had four clear chances, you don’t normally see that many in a final, so that means a lot,” said the Chelsea boss.
“For some players coming back, like Frank Lampard, it will be an improvement on his match fitness. For others, it will be a good experience; they will know what it’s like to play against a strong South American team and to play in another continent with a different atmosphere.”
Benítez, however, did acknowledge that his side were often overpowered by a physical display by their opponents.
“They were very physical from the first minute with every challenge and every second ball,” he continued. “As soon as they scored, they were passing and keeping the ball which made it difficult.
“You can analyse the game, but we created four very good chances, which is a lot, their goalkeeper was the best player on the pitch.
“We knew we would have chances in between the lines. We had possession and very good counter-attacks but it’s a question of taking your chances.”
MORE: Man United latest news
MORE: Arsenal latest news
MORE: Chelsea latest news
MORE: Liverpool latest news